Variable copy number, intra-genomic heterogeneities and lateral transfers of the 16S rRNA gene in Pseudomonas.
Variable copy number, intra-genomic heterogeneities and lateral transfers of the 16S rRNA gene in Pseudomonas.
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DOI：
10.1371/journal.pone.0035647
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Quillet L
中科院分区：
文献类型：
--
作者：
Bodilis J;Nsigue-Meilo S;Besaury L;Quillet L
尽管16S rRNA基因是微生物生态学中最常用的分类标记，但在属内水平上对16S rRNA基因的分辨率仍然不高。在这项工作中，对整个假单胞菌属的rRNA基因操纵子的数量、基因组内的异质性和横向转移进行了精细分辨率的研究。除19株已测序的假单胞菌外，我们还用Southern杂交和脉冲场凝胶电泳法测定了另外4株假单胞菌的16S rRNA拷贝数，并用变性梯度凝胶电泳法和测序法研究了其基因组内的异质性。虽然可变拷贝数(从4个到7个)似乎与进化距离有关，但荧光假单胞菌谱系中一些接近的菌株显示了不同数量的16S rRNA基因，而所有铜绿假单胞菌谱系中的所有菌株都显示了相同数量的基因(4个副本)。进一步的基因组内异质性研究表明，大多数假单胞菌(19株中的15株)至少有两个不同的16S rRNA等位基因。只有在两个测序菌株中观察到了巨大的差异(5或19个核苷酸，基本上集中在V1高变区附近)。在我们研究的一个菌株(MFY30菌株)中，我们发现16S rRNA基因的拷贝之间存在12个核苷酸的差异(集中在V3高变区)。最后，在数据库中可获得的1803株假单胞菌的全长序列中，进一步研究了16S rRNA基因的部分侧向转移的发生。值得注意的是，我们发现至少48.3%和41.6%的16S rRNA序列的最大可变区(V1和V3高变区)可能是从另一个进化较远的假单胞菌株横向转移过来的。总之，我们强烈建议在属内多样性研究中删除16S rRNA基因的这些区域。
Even though the 16S rRNA gene is the most commonly used taxonomic marker in microbial ecology, its poor resolution is still not fully understood at the intra-genus level. In this work, the number of rRNA gene operons, intra-genomic heterogeneities and lateral transfers were investigated at a fine-scale resolution, throughout the Pseudomonas genus. In addition to nineteen sequenced Pseudomonas strains, we determined the 16S rRNA copy number in four other Pseudomonas strains by Southern hybridization and Pulsed-Field Gel Electrophoresis, and studied the intra-genomic heterogeneities by Denaturing Gradient Gel Electrophoresis and sequencing. Although the variable copy number (from four to seven) seems to be correlated with the evolutionary distance, some close strains in the P. fluorescens lineage showed a different number of 16S rRNA genes, whereas all the strains in the P. aeruginosa lineage displayed the same number of genes (four copies). Further study of the intra-genomic heterogeneities revealed that most of the Pseudomonas strains (15 out of 19 strains) had at least two different 16S rRNA alleles. A great difference (5 or 19 nucleotides, essentially grouped near the V1 hypervariable region) was observed only in two sequenced strains. In one of our strains studied (MFY30 strain), we found a difference of 12 nucleotides (grouped in the V3 hypervariable region) between copies of the 16S rRNA gene. Finally, occurrence of partial lateral transfers of the 16S rRNA gene was further investigated in 1803 full-length sequences of Pseudomonas available in the databases. Remarkably, we found that the two most variable regions (the V1 and V3 hypervariable regions) had probably been laterally transferred from another evolutionary distant Pseudomonas strain for at least 48.3 and 41.6% of the 16S rRNA sequences, respectively. In conclusion, we strongly recommend removing these regions of the 16S rRNA gene during the intra-genus diversity studies.
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